Reef fish assemblages: a re-evaluation using enclosed rotenone stations

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m2 quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities.

A quantitative examination of the reef fish assemblage at Orpheus Island, Great Barrier Reef, contrasting clove oil and rotenone, sampled 365 individuals of 47 species with clove oil v. 536 individuals of 53 species with rotenone. Number of species and individuals were not found to differ significantly between the two techniques, largely due to variation among samples. Neopomacentrus bankieri (Pomacentridae) and Eviota queenslandica (Gobiidae) were the most dominant in the samples using either technique. Although the samples appeared to be comparable, only 31 species (45%) in eight families were common to both techniques. Fishes often recovered before collection when using clove oil and were not driven out of the reef during induction to anaesthesia. Although the samples collected with clove oil approximate the results obtained using rotenone, enclosed rotenone stations are the preferred method for providing relatively complete quantitative samples.

A quantitative examination of the reef fish assemblage at Orpheus Island, Great Barrier Reef, contrasting clove oil and rotenone, sampled 365 individuals of 47 species with clove oil v. 536 individuals of 53 species with rotenone. Number of species and individuals were not found to differ significantly between the two techniques, largely due to variation among samples. Neopomacentrus bankieri (Pomacentridae) and Eviota queenslandica (Gobiidae) were the most dominant in the samples using either technique. Although the samples appeared to be comparable, only 31 species (45%) in eight families were common to both techniques. Fishes often recovered before collection when using clove oil and were not driven out of the reef during induction to anaesthesia. Although the samples collected with clove oil approximate the results obtained using rotenone, enclosed rotenone stations are the preferred method for providing relatively complete quantitative samples.

Oceanographic influences on reef fish assemblages along the Great Barrier Reef

The present research quantitatively compared the fish composition among two methods for non-cryptic benthic fish species and one method for cryptobenthic fish species for the first time for the Mediterranean temperate reef fish assemblage. A visual census of fishes was performed within a cylinder of 4 m radius and within a cylinder of 2 m radius, while the cryptobenthic fishes were collected using a square of 1 m2 with anesthetic. The data and material were collected at fifty sampling points. The visual census methods together recorded 31 species, and the square with anesthetic method recorded 18 species. The quantitative comparison of methods of visual census and cryptobenthic fish collecting showed significantly different species richness, total fish abundance, and fish assemblage structure among methods. The applied methods were highly complementary. The cylinder of 2 m radius is well suited for epibenthic fishes and the cylinder of 4 m radius is reliable for hyperbenthic and benthopelagic fishes. Therefore, each of the methods well covered one of three components of ichthyobenthos (hyperbenthic, epibenthic, and cryptobenthic fishes), and all three methods together provided a far more complete assessment of fish species composition than any individual census method for the Mediterranean littoral benthic fishes.

Reef fish assemblage structure affected by small-scale spacing and size variations of artificial patch reefs

There is an increasing concern that invasive lionfish will have dramatic impacts on native reef fish assemblages in the Caribbean. However, the intensity and speed of such changes will probably depend on the initial structure of each assemblage and on the lionfish population characteristics. The species composition of native fishes, diet and size structures were analyzed on a protected Venezuelan reef, through visual census on zones with and without lionfish, 1 and 3 years after the first sighting of Pterois (lionfish). Lionfish mean density ± SD increased from 30 ± 83.5 (n = 22) to 121 ± 164 ind ha−1 (n = 22), with an important increase in lionfish over 30 cm and the near absence of juveniles. Native species richness and densities remained stable through time. No significant change of native fish assemblage structure, species richness and density of potential Pterois prey, predators and competitors was found over time, but zones with lionfish had significantly higher levels of prey and predators, and significantly different fish assemblage structures. Most importantly, there was no interaction between time and the presence of Pterois on these metrics. Our results may suggest that: 1—a healthy composition of the initial structure of the reef fish assemblage may moderate the early impact of lionfish, and the observed lionfish densities (mean ± SD = 121 ± 164 ind ha−1, n = 22) were not sufficient to induce a significant change in the assemblage; and 2—lionfish probably select zones where species richness and density of prey are the highest.

We examined the pattern of development of assemblages of coral reef fishes on artificial reefs at One Tree Reef, Great Barrier Reef. Two sets of 8 reefs were built. To investigate the effects of habitat structure on species diversity, each set consisted of replicate pairs of 4 different reef types: plain (no holes), small—holed, medium—holed, and large—holed reefs. To examine seasonal differences in colonization, 1 set was established in summer (October 1971) and the other set in winter (July 1972). Visual censuses of the reefs' fish assemblages were made at monthly intervals over 32 mo (summer set) and 23 mo (winter set). We recorded a total of 105 resident species from the artificial reefs. Although less diverse, the fish assemblages differed little in terms of species composition from those of small natural patch reefs. Artificial reefs showed a high between—reef variability in species composition that was largely unrelated to habitat structure. Competitive interactions between species appeared unimportant in explaining the distribution of species between reefs. Likewise, possible positive associations between species were indicated for only a few species. Almost all settlement of the artificial reefs was by juvenile fishes. Recruitment was markedly seasonal and occurred mainly over summer (September—May). Juvenile recruitment patterns showed little year—to—year constancy. Most species tested showed nonrandom, clumped patterns of settlement on replicate reefs. More than half of species tested showed no significant differences on numbers of individuals which settled on different reefs, but the remainder showed significantly greater settlement on some reefs, suggesting habitat selection. For a few species, there was also greater recruitment to reefs already occupied by conspecifics, suggesting possible social facilitation of settlement. For most species, there were no significant interspecific interactions between adults and newly settling juveniles. Between—census variability in species composition was high and species turnover ranged from °17% of species/mo in winter to °39% in summer. Maximum times of persistence for most species were <12 mo, and for many individuals survivorship was of the order of only a few months. Much of the high turnover appears due to losses through predation. There was no evidence that a persistent species equilibrium was attained during colonization. Because of predation and the seasonally varying, uncertain nature of recruitment, we see the development of any long—term species equilibrium as unlikely. We suggest that nonequilibrium conditions are a characteristic of coral reef fish communities and that because of these conditions, high within—habitat diversities are maintained.

In the Anthropocene, understanding and managing ecological communities requires the characterization of natural spatiotemporal ecosystem dynamics. Complex ecosystems may appear chaotic and unstructured, making long‐term monitoring programs with hierarchical sampling designs ideal for investigating ecological patterns at multiple scales. Here, we use a dataset spanning the entire Great Barrier Reef (GBR) and multiple decades to determine the spatial patterns of distribution and abundance, and how these change through time, in 233 reef‐associated fish species. Community composition was strongly structured by position across the continental shelf, with distinct inner and outer shelf assemblages. Latitudinal differences were smaller, except for the distinctive assemblages of the southernmost Swain and Capricorn‐Bunker regions. GBR‐wide summaries of total density and species richness did not show directional shifts, and it was only after analyzing these metrics at the subregional scale that a wider range of temporal oscillations was identified, indicating that responses of fish assemblages to perturbations require examination of smaller than GBR scales. Within most subregions (65%), fish species composition has undergone a clear and ongoing directional shift away from the community identified in the 1990s. These changes were generally due to a reduction in the numbers of coral‐dependent species and an increased dominance of grazers and generalists. Among the 233 species, there have been more “winners” than “losers” across the whole GBR, but this masks a tendency for inner shelf reefs of the central GBR to have a dominance of “losers” over time. Reef fish assemblages on the GBR are dynamic and show clear recovery potential from disturbance events. Despite some pervasive community‐level shifts in the last decades, the clear biogeographic characteristics of each subregion remain intact. We pose the question of whether it is reasonable to expect these highly dynamic assemblages to reach a relatively stable “climax community,” and posit that the answer is scale‐dependent and, on the GBR, is currently resolved at the subregional scale, which is the scale at which most stakeholders and decision‐makers operate.

Spatial variability in habitat structure and heterogenic coral reef fish assemblages inside a small-scale marine reserve after a coral mass mortality event

Reliable abundance estimates for species are fundamental in ecology, fisheries, and conservation. Consequently, predictive models able to provide reliable estimates for un- or poorly-surveyed locations would prove a valuable tool for management. Based on commonly used environmental and physical predictors, we developed predictive models of total fish abundance and of abundance by fish family for ten representative taxonomic families for the Great Barrier Reef (GBR) using multiple temporal scenarios. We then tested if models developed for the GBR (reference system) could predict fish abundances at Ningaloo Reef (NR; target system), i.e., if these GBR models could be successfully transferred to NR. Models of abundance by fish family resulted in improved performance (e.g., 44.1% <R2 < 50.6% for Acanthuridae) compared to total fish abundance (9% <R2 < 18.6%). However, in contrast with previous transferability obtained for similar models for fish species richness from the GBR to NR, transferability for these fish abundance models was poor. When compared with observations of fish abundance collected in NR, our transferability results had low validation scores (R2 < 6%, p > 0.05). High spatio-temporal variability of patterns in fish abundance at the family and population levels in both reef systems likely affected the transferability of these models. Inclusion of additional predictors with potential direct effects on abundance, such as local fishing effort or topographic complexity, may improve transferability of fish abundance models. However, observations of these local-scale predictors are often not available, and might thereby hinder studies on model transferability and its usefulness for conservation planning and management.

Aim We examined comparative data for cryptobenthic reef fishes to determine how variation in regional species richness relates to local species richness, abundance, and taxonomic and trophic composition, and to test whether systems with higher species richness exhibit finer habitat partitioning.Locations Lizard Island, Great Barrier Reef (GBR), Australia; Bahía de Loreto, Gulf of California (GoC), Mexico.Methods Cryptobenthic reef fish assemblages from four habitats (coral heads, rubble, and horizontal and vertical surfaces of boulders) were collected using clove oil. Differences in density, species richness and biomass were examined between regions and among habitats. Habitat associations were identified for each habitat/location based on multivariate ordination, and the statistical significance of patterns was tested using analysis of similarity (ANOSIM). In addition, the trophic group composition of the assemblages for both regions was examined.Results A total of 91 species in 20 families were recorded (GBR, 66 species; GoC, 25 species). Total and habitat species richness were higher on the GBR, whereas biomass was higher in the GoC. No difference in fish density between regions was found. Habitat division among assemblages was greater in the depauperate GoC. Only coral head associations proved to be distinctive on the GBR, whereas three sample groups were found in the GoC (coral heads, horizontal boulders and vertical boulders/rubble). Trophic composition in the two regions was markedly different, with omnivores dominating the GBR fauna and planktivores the GoC.Main conclusions A positive regional–local relationship in fish diversity was found between regions, but fish abundance in both regions remained similar. Contrary to expectations, habitat partitioning, at a community level, was greater in the depauperate GoC. Differences in trophic composition and patterns of habitat use appear to reflect the disparate history of the regions, whereas patterns of abundance may reflect the influence of fundamental relationships between size and abundance in communities. This study highlights the potential of reef faunas to conform to universal numerical trends while maintaining an ability to respond ecologically to local/evolutionary influences. The GoC fauna appears to be exceptionally vulnerable to natural and anthropogenic disturbance owing to the high numerical dominance of habitat‐specific species and to the limited potential for functional redundancy within the system.

Spatial variation in the epilithic algal matrix (EAM) cryptofauna was investigated at three locations on the Great Barrier Reef: two inner shelf—Orpheus Island and the Turtle Island group—and a mid-shelf location, Lizard Island. Although the EAM appears to be a relatively simple and consistent habitat, significant differences in cryptofaunal assemblages were found between locations. EAM assemblages from Orpheus Island were markedly different. This appears to be a function of the sediment profile characteristics (grain size >60 µm) at Orpheus Island, as many cryptofaunal taxa displayed positive relationships with sediment volume. However, sediment volumes did not differ significantly between the three locations, highlighting the possibility of cyclonic activity affecting the sediment profile at Orpheus Island in the months preceding the study, in addition to the nutrient input from major terrigenous sources. The results of this study show that EAM cryptofaunal assemblages are not uniform across the Great Barrier Reef and suggest that dissolved nutrients, sediment loads and distance from river systems may be significant drivers of cryptobenthic faunal compositions.

Understanding how co-occurring species within comparable trophic guilds (sympatry) partition resources provides fundamental information about their ecological roles within an ecosystem. Despite morphological and biological similarities, resources may be selected and exploited independently, leading to alternative interactions and influences within the ecosystem. Studying movement and dietary patterns directly relates to an animal's resource use, and is a valuable approach to characterise preferred prey and habitat within and between sympatric species. Expanding knowledge of resource use is essential to address how animals are affected by, and how they might respond to, an increasingly variable environment, and is necessary to implement ecosystem-based management practices. Coral trout or coralgrouper (Plectropomus spp.) are iconic and economically significant mesopredatory reef fishes within Australia's Great Barrier Reef (GBR) and throughout the Indo-Pacific region. Despite the importance of Plectropomus spp. in the Queensland Coral Reef Fin Fish Fishery, investigations focussed on their ecology are surprisingly limited. Much of the behavioural-based research has been conducted in scenarios of captivity, is biased by confounding sampling limitations, or only provides short-term, data-poor perspectives. Consequently, interpretations of findings are often applicable only to certain periods or locations, or are only based on patterns from a small number of individuals. This hinders the ability of managers to evaluate how fishing pressure, protection initiatives, and environmental fluctuations or disturbances might impact populations. Furthermore, research is overwhelmingly directed at P. leopardus (or grouped as Plectropomus spp.) which forms the majority of commercial catches on the GBR. Nevertheless, other species such as P. maculatus and P. laevis are readily captured by both recreational and commercial sectors, but their resource selection patterns and interactions with P. leopardus are unknown. The research in this thesis employed two methodological approaches – passive acoustic telemetry and stable isotope analysis, to study movement and dietary patterns, respectively, in three exploited species of coral trout – P. leopardus, P. maculatus, and P. laevis. The research was conducted at three primary locations – Orpheus Island, four mid-shelf/offshore reefs in the Townsville region (Townsville reefs), and the Marine and Aquaculture Research Facilities Unit (MARFU) at James Cook University. Samples and data were collected over the course of three years (2013-2015) providing extensive ecological and behavioural information from more than 300 individual Plectropomus. The overall aim of this research was to quantify, qualify, and compare long-term movement and dietary patterns of sympatric Plectropomus spp. By using multiple approaches, this thesis showed that broad resource selection trends differ between sympatric species, but interestingly, the way they differ is unique to each species pairing. At the Townsville reefs, P. laevis moved greater distances and had increased variability in depth use compared to P. leopardus. Movement patterns were correlated with distinct dietary niches between species, particularly when colour phases of P. laevis (footballer and blue-spot) were separated. The limited isotopic niche overlap between species was not correlated with fish size, indicating alternate prey selection, feeding styles, or energetic requirements engrained at a species level. Based on results from an aquarium-based stable isotope feeding trial, the trophic position of P. leopardus in the wild varied little between sampling locations and time periods. Similarly, the isotopic niches between species remained constant for several tissues (a proxy to feeding timeline) and at several reefs, suggesting feeding pressures exerted by each species is consistent within the region. Consequently, it is hypothesised that both P. laevis and P. leopardus will respond to environmental or humaninduced disturbances in similar ways within and across compatible reefs. At Orpheus Island, P. maculatus shared the same home range size as P. leopardus, however P. maculatus remained deeper in the water column throughout daily and monthly periods. These spatial patterns were correlated to overlapping isotopic niches - or similar prey selection. These trends indicate a high potential for competition that may be mediated by spatial or habitat partitioning. Overall, this research highlights the need for greater species-specific consideration relative to conservation and management initiatives since Plectropomus spp. readily demonstrate distinct behavioural patterns, and will likely respond to disturbances differently. Without fundamental knowledge of how co-occurring species select and partition resources, their interactions and impacts throughout the reef ecosystem remain unknown. Not only did this thesis provide new information about each species, it produced preliminary evidence that interactions between species may shape how resources are utilised on coral reefs.

Decades of monitoring have informed the stewardship and ecological understanding of Australia's Great Barrier Reef